User: Rory Stark

gravatar for Rory Stark
Rory Stark2.8k
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CRUK, Cambridge, UK
Last seen:
2 weeks, 1 day ago
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6 years, 2 months ago
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r*********@cruk.cam.ac.uk

I am Principal Scientist, Computational Biology at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 475 results • page 1 of 48 • next >
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Answer: A: Can I input peak files from Genrich as input reads in DiffBind?
... Yes, this should work with the `.narrowPeak` files. In the sample sheet, the values in the `PeakCaller` column should be set to `"narrow"`. ...
written 4 weeks ago by Rory Stark2.8k
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Comment: C: How to produce the fraction of reads in peaks (FRiP) using DiffBind
... > atac <- dba(sampleSheet = "atac.csv", bRemoveM = TRUE, bRemoveRandom = FALSE, bCorPlot = TRUE, peakFormat = "narrow") > dba.save(atac,"atac_peaks") > atac <- dba.count(atac, minOverlap = 1) > dba.save(atac,"atac_counts") which will create ...
written 4 weeks ago by Rory Stark2.8k
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Answer: A: Using DiffBind with only a counts table?
... You can import count data directly into DiffBind using the `Counts` column in the sample sheet. This is documented in the help page for dba.peakset(). It assume you have already generated a consensus peakset (same intervals for each sample) and counted the reads in each interval, so that you have a ...
written 4 weeks ago by Rory Stark2.8k
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Answer: A: How to produce the fraction of reads in peaks (FRiP) using DiffBind
... Hmmn, for some reason the `FRiP` values are not being computed by `dba.count()`, or else they would have shown up then you listed the DBA object `atac` after counting. If you can send me copies of the DBA object `atac` before and after the call to `dba,count()` (or a link where I can download them), ...
written 4 weeks ago by Rory Stark2.8k
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Answer: A: DiffBind peaks input file format
... In the `summit.bed` files, the intervals are all only one base wide, while in the `.xls` file, the peaks are much wider and of variable width. As the pre-counting correlations are based on overlaps, there will be very little overlap when using `summit.bed` files. This same problem will limit the num ...
written 6 weeks ago by Rory Stark2.8k
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Answer: A: DiffBind with highly variable FRiP (Fraction Reads in Peaks)
... If you have a prior expectation of a unidirectional shift in signal intensity toward one sample group (the disease condition), you should avoid normalizing use an RNA-seq method that assumes that there is a core of sites that don't change, and that changes will occur in both directions. The defaul ...
written 6 weeks ago by Rory Stark2.8k
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Answer: A: DiffBind - Counting reads - counts not found
... It looks like you are following the vignette script very closely, but given that you are working with another dataset, some of the specific references do not apply. In the first line you are reading in a samplesheet. In the vignette, the example samplesheet is included with the package installation ...
written 6 weeks ago by Rory Stark2.8k
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Answer: A: Diffbind plotting options
... In the call to `dba.plotPCA()`, set `attributes=DBA_CONDITION` (instead of `label`). You can set `label` to something else if that is helpful. For example, consider the sample data: data(tamoxifen_counts) tamoxifen <- dba.contrast(tamoxifen, gr ...
written 6 weeks ago by Rory Stark2.8k
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Answer: A: Handing duplicates in DiffBind
... If you want to remove duplicates, you need to mark duplicates before running `dba.count()`, whatever `bUseSummarizeOverlaps` is set to. If duplicated are not marked, even if you set `bRemoveDuplicates=TRUE`, no duplicates will be identified. However for differential analysis, we strongly recommend ...
written 6 weeks ago by Rory Stark2.8k
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Answer: A: how to retrieve binding affinity matrix in diffbind
... counts <- dba.peakset(myDBA, bRetrieve=TRUE, writeFile="myFile.csv") You will get back the normalized count scores; you can get raw read counts by changing the value for the `score` parameter in `dba.count()`. ...
written 8 weeks ago by Rory Stark2.8k

Latest awards to Rory Stark

Popular Question 5 months ago, created a question with more than 1,000 views. For diffbind
Scholar 5 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 6 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Differential analysis of multiple samples with different time points
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: diffbind finding not differential site
Scholar 6 months ago, created an answer that has been accepted. For A: DiffBind differential binding normalization with different levels of binding
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Scholar 8 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 11 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: Diffbind - What exactly is a "consensus" peak set?
Scholar 22 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 22 months ago, created an answer that has been accepted. For A: DiffBind matrix of values
Popular Question 22 months ago, created a question with more than 1,000 views. For diffbind
Popular Question 22 months ago, created a question with more than 1,000 views. For DiffBind Question
Popular Question 22 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 22 months ago, created an answer that has been accepted. For A: DiffBind MA plot
Scholar 22 months ago, created an answer that has been accepted. For A: DiffBind dba.analyze() to return all differentially enriched peaks?
Scholar 22 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 22 months ago, created an answer that has been accepted. For A: Diffbind and dba.peakset vs dba.overlap
Scholar 22 months ago, created an answer that has been accepted. For A: DiffBind - Losing replicate information?
Scholar 22 months ago, created an answer that has been accepted. For A: Diffbind: dba.plot retrieve variance explained
Scholar 22 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 22 months ago, created an answer that has been accepted. For A: DiffBind Heatmap Omitting Results?
Popular Question 22 months ago, created a question with more than 1,000 views. For minOverlap in DiffBind in R- what does it mean?
Scholar 22 months ago, created an answer that has been accepted. For A: Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind

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